Package index • gp3bayes

Package overview

gp3bayes gp3bayes-package: gp3bayes: Contract-First Bayesian Workflows for Hierarchical Behavioural Data

Model contracts

create_model_contract(): Create an Approved Bayesian Model Contract

Readiness audits

audit_model_readiness(): Audit Data Readiness for an Approved Model Contract

Model specifications

build_model_formula(): Build an Approved Model Formula
create_prior_specification(): Create a Backend-Independent Prior Specification
validate_prior_specification(): Validate a Prior Specification
create_model_specification(): Create a Complete Model Specification

Binary workflow foundation

simulate_hierarchical_binary_data(): Simulate Hierarchical Binary Data
prepare_hierarchical_binary_data(): Prepare Hierarchical Binary Data
specify_binary_model(): Specify a Backend-Independent Binary Model
check_binary_prior_predictive(): Check Binary Prior Predictive Behaviour

Binary model fitting

translate_binary_model_to_brms(): Translate a Binary Model Specification to brms
fit_binary_model(): Fit an Approved Hierarchical Binary Model

Binary posterior validation

diagnose_binary_fit(): Diagnose a Fitted Binary Model
summarise_binary_posterior(): Summarise a Binary Posterior
check_binary_posterior_predictive(): Check Binary Posterior Predictive Behaviour
assess_binary_prior_sensitivity(): Assess Binary Prior Sensitivity
run_binary_recovery(): Run Binary Parameter Recovery
create_binary_model_report(): Create a Structured Binary Model Report
plot_sampling_diagnostics(): Plot Sampling Diagnostics

Lognormal duration workflow

simulate_hierarchical_duration_data(): Simulate Hierarchical Lognormal Duration Data
prepare_hierarchical_duration_data(): Prepare Hierarchical Duration Data
specify_duration_model(): Specify a Backend-Independent Duration Model
check_duration_prior_predictive(): Check Duration Prior Predictive Behaviour
translate_duration_model_to_brms(): Translate a Duration Model Specification to brms
fit_duration_model(): Fit an Approved Hierarchical Lognormal Duration Model

Duration posterior validation

diagnose_duration_fit(): Diagnose a Fitted Duration Model
summarise_duration_posterior(): Summarise a Duration Posterior
check_duration_posterior_predictive(): Check Duration Posterior Predictive Behaviour
assess_duration_prior_sensitivity(): Assess Duration Prior Sensitivity
run_duration_recovery(): Run Duration Parameter Recovery
create_duration_model_report(): Create a Structured Duration Model Report

Advanced optional workflows

bayesian_backend_capabilities(): Report Optional Bayesian Backend Capabilities
check_cmdstan_backend(): Check the CmdStanR Backend
specify_binary_model_with_interaction_prior(): Specify a Binary Model with a Separate Interaction Prior
specify_duration_model_with_interaction_prior(): Specify a Duration Model with a Separate Interaction Prior
interaction_prior_summary(): Summarise Separate Interaction Prior Metadata
translate_binary_model_with_interaction_prior(): Translate an Advanced Binary Specification to brms
translate_duration_model_with_interaction_prior(): Translate an Advanced Duration Specification to brms
fit_binary_model_backend() fit_binary_model_cmdstanr(): Fit a Binary Model with a Selected Full-MCMC Backend
fit_duration_model_backend() fit_duration_model_cmdstanr(): Fit a Duration Model with a Selected Full-MCMC Backend
detect_binary_separation(): Detect Separation in the Binary Fixed-Effects Screen
compute_psis_loo(): Compute PSIS-LOO for a gp3bayes Fit
compute_psis_loo_from_log_lik(): Compute PSIS-LOO from a Log-Likelihood Matrix
identify_loo_influential_observations(): Identify Influential PSIS-LOO Observations
compare_psis_loo(): Compare Models with PSIS-LOO
compute_loo_model_weights(): Compute LOO Model-Averaging Weights
assess_powerscaled_sensitivity(): Assess Power-Scaled Prior and Likelihood Sensitivity
powerscale_sequence_for_fit(): Create a Power-Scaling Sequence
simulate_binary_pathology(): Simulate a Dedicated Binary Pathology Scenario
simulate_duration_pathology(): Simulate a Dedicated Duration Pathology Scenario
evaluate_pathological_simulation(): Evaluate a Pathological Simulation Against the Contract Gate
create_brms_sbc_plan(): Create a brms-Based Simulation-Based Calibration Plan
create_custom_sbc_plan(): Create an Expert Custom SBC Plan
run_sbc_plan(): Run a Simulation-Based Calibration Plan
summarise_sbc_result(): Summarise an SBC Result

Specification closure

summarise_condition_balance(): Summarise Overall Condition Balance
summarise_binary_group_variation(): Summarise Binary Outcome Variation Within Groups
identify_identifier_like_predictors(): Identify Identifier-Like Numeric Predictors
review_duration_extremes(): Review Extreme Positive Durations Without Deleting Them
audit_duration_boundaries(): Audit Duration Range and Censoring Boundaries
audit_model_readiness_strict(): Run a Strict Model-Readiness Audit
plot(<gp3bayes_strict_readiness_audit>): Plot a Strict Readiness Audit
create_transformation_recipe(): Create a Reusable Transformation Recipe
apply_transformation_recipe(): Apply a Recorded Transformation Recipe
invert_transformation_recipe(): Invert a Recorded Transformation Recipe
validate_transformation_replay(): Validate Exact Transformation Replay
estimate_standardized_probability_contrast(): Estimate a Design-Standardised Binary Probability Contrast
estimate_standardized_duration_estimands(): Estimate Design-Standardised Duration Estimands
summarise_estimand_draws(): Summarise Posterior Estimand Draws
create_random_slope_sensitivity_plan(): Create a Random-Slope Sensitivity Plan
run_random_slope_sensitivity(): Run Random-Intercept versus Random-Slope Sensitivity
create_group_deletion_sensitivity_plan(): Create a Group-Deletion Sensitivity Plan
run_group_deletion_sensitivity(): Run a Group-Deletion Sensitivity Plan
compare_estimand_sensitivity(): Compare Estimand Sensitivity Across Alternative Fits
audit_estimand_invariance(): Audit Estimand Invariance Against a Declared Tolerance
create_contrast_coding_sensitivity_specification(): Create a Contrast-Coding Sensitivity Specification
create_predictor_scaling_sensitivity_specification(): Create a Predictor-Scaling Sensitivity Specification
create_duration_unit_sensitivity_specification(): Create a Duration-Unit Sensitivity Specification
audit_duration_unit_invariance(): Audit Duration-Unit Invariance
check_binary_ppc_details(): Run Detailed Binary Posterior Predictive Checks
check_duration_ppc_details(): Run Detailed Duration Posterior Predictive Checks
compute_kfold_cv(): Compute Governed Exact K-Fold Cross-Validation
plot(<gp3bayes_kfold_cv>): Plot Governed Exact K-Fold Results
gp3bayes_specification_traceability(): Specification-Closure Traceability Matrix